Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape


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Documentation for package ‘BBMV’ version 2.1

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BBMV-package Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape
ACE_FPK Ancestral Character Estimation
add.ML.landscape.FPK Plot macroevolutionary landscapes estimated by the FPK or BBM+V models
BBMV Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape
charac_time Characteristic time measurement
ConvProp_bounds Convolution of the diffusion matrix with the trait density vector.
DiffMat_backwards Diffusion matrix building
DiffMat_forward Diffusion matrix building
find.mle_FPK Maximum-likelihood estimation
find.mle_FPK_multiple_clades_same_V_different_sig2 Maximum-likelihood estimation
find.mle_FPK_multiple_clades_same_V_same_sig2 Maximum-likelihood estimation
fit_BBMV_multiple_clades_different_V_different_sig2 Fit independent models in several clades.
fit_FPK_multiple_clades_different_V_different_sig2 Fit independent models in several clades.
FormatTree_bounds Tree formatting.
FPK_sim_traitgram Simulations with traitgram
get.landscape.FPK Plot macroevolutionary landscapes estimated by the FPK or BBM+V models
get.landscape.FPK.MCMC Plot posterior distribution of macroevolutionary landscapes.
lnL_BBMV Creation of the likelihood function
lnl_BBMV_multiclades_same_V_different_sig2 Likelihood functions for multiple clades
lnl_BBMV_multiclades_same_V_same_sig2 Likelihood functions for multiple clades
lnL_FPK Creation of the likelihood function
lnl_FPK_multiclades_same_V_different_sig2 Likelihood functions for multiple clades
lnl_FPK_multiclades_same_V_same_sig2 Likelihood functions for multiple clades
LogLik_bounds Likelihood of the FPK model
LogLik_bounds_est_root Likelihood of the FPK model
log_prior_5pars_root_bounds Prior function.
log_prior_nclades_plus_3_pars Prior function.
MH_MCMC_FPK MCMC estimation
MH_MCMC_FPK_multiclades MCMC estimation on multiple clades
posterior_vs_prior Posterior vs. prior comparison for the FPK model.
prep_mat_exp Matrix exponential.
proposal_5pars_root_bounds Parameter update for the MCMC function
proposal_nclades_plus_3_pars Parameter update for the multiclade MCMC function
reformat_multiclade_results Format the output of a multiclade fit
Sim_FPK Simulation of the BBM+V process.
trans_from_fixed Linear transformations
trans_to_fixed Linear transformations
Uncertainty_FPK Parameter uncertainty
VectorPos_bounds Discretization of a continuous trait value into a probability vector.